| 2012 | AMIA | Risk Stratification of ICU Patients Using Topic Models Inferred from Unstructured Progress Notes. | Li-Wei H. Lehman, Mohammed Saeed, William J. Long, Joon Lee, Roger G. Mark |
| 2007 | AMIA | Lessons Extracting Diseases from Discharge Summaries. | William J. Long |
| 2006 | AMIA | Natural Language Processing of Spoken Diet Records (SDRs). | Ronilda C. Lacson, William J. Long |
| 2003 | AMIA | Parsing Free Text Nursing Notes. | William J. Long |
| 2000 | AMIA | New approaches to measuring the performance of programs that generate differential diagnoses using ROC curves and other metrics. | Hamish Fraser, Shapur Naimi, William J. Long |
| 2000 | AMIA | Developing a Program for Tracking Heart Failure. | William J. Long, Hamish Fraser, Shapur Naimi, Kathleen Perry, Linda Cotter, Marvin A. Konstam |
| 1999 | AMIA | CompareDx: a Software Toolkit for Measuring the Performance of Programs that Generate Multiple Diagnoses. | Hamish S. F. Fraser, William J. Long |
| 1999 | AMIA | Evaluating a Decision Support System Using the Web. | Hamish S. F. Fraser, William J. Long, Shapur Naimi |
| 1999 | AMIA | The Heart Disease Program: Assisting Diagnosis. | William J. Long, Hamish Fraser, Shapur Naimi |
| 1998 | AMIA | Differential diagnoses of the heart disease program have better sensitivity than resident physicians. | Hamish S. F. Fraser, William J. Long, Shapur Naimi |
| 1998 | AMIA | Interfacing the Heart Disease Program to Coded Data. | William J. Long, Hamish Fraser, Shapur Naimi |
| 1997 | AMIA | Comparing Complex Diagnoses: A Formative Evaluation of the Heart Disease Program. | Hamish S. F. Fraser, William J. Long, Shapur Naimi |
| 1997 | AMIA | Collecting and Interpreting Temporal Data in an Expert System. | William J. Long, Hamish Fraser, Shapur Naimi, James E. Stahl |
| 1983 | AAAI | Reasoning About State From Causation and Time in a Medical Domain. | William J. Long |
| 1983 | IJCAI | A Control Structure for Time Dependent Reasoning. | William J. Long, Thomas A. Russ |